Microsoft Windows is unable to read any other type of partitions apart from FAT, Fat12, FAT16, FAT32, NTFS.
This is especially true for Microsoft Windows 2000 and below. I believe XP Professional behaves somewhat differently.
What you're seeing is likely to be Windows Setup being unable to continue due to 'insufficient disk space' because of this.
You'll have to free up disk space by resizing partitions and/or creating an empty FAT partition of suitable size before you run Windows Setup again to avoid any anomalies.
Then again on the other side, has this laptop ever run Microsoft Windows at all? is it equipped with SATA harddisk interfaces? (if yes you probably need to load drivers during setup, or alter BIOS settings, use a custom Windows Setup bootdisk, etc.)
You could also check with the manual/manufacturer of your laptop to see what is necessary for Windows Setup to proceed normally.
Some BIOS settings such as the ones found in Power Management (S1,S3, Auto?) and Advanced BIOS settings (APIC Mode?) can also stall or abort Windows Setup prematurely.
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